fantom_to_expset {GAPGOM} | R Documentation

## GAPGOM - fantom_to_expset()

### Description

Convert raw data.table/data.frame fantom5 object to a proper ExpressionSet.

### Usage

    fantom_to_expset(fanraw, species, filter = TRUE, verbose = FALSE)

### Arguments

`fanraw` | raw data.table object from the fantom_load_raw() function.
`species` | either "human" or "mouse". This is important because both datasets have different metadata/stats
`filter` | Filter, this causes only entries to be added that have an entrez ID. Normally this should be left on default (TRUE) because all algorithms in this library need the entrez IDs for translation.
`verbose` | Switch to TRUE for extra messages. Default=FALSE

### Details

This function converts fantom5 data and converts it into an ExpresionSet. This ExpressionSet is then returned. This function only accepts the RLE normalized data!

### Value

The resulting ExpressionSet contains the original data. The expressiondata can be found under assayData(ExpressionSet)[["exprs"]] Other information (first 6 info columns) can be found under; pData(featureData(ExpressionSet))

### Examples

    fantom_file <- fantom_download(organism = "mouse", noprompt = TRUE)
    ft5 <- fantom_load_raw(fantom_file, verbose = TRUE, example = TRUE)
    expset <- fantom_to_expset(ft5, "mouse", verbose = TRUE)

[Package GAPGOM version 1.0.0 Index]